tbuckley/cabot-search huggingface dataset:
Inorganic nanoparticle‐integrated mesenchymal stem cells: A potential biological agent for multifaceted applications
Authors: Juan‐Juan Zheng, Xin‐Chi Jiang, Yao‐Sheng Li, Jian‐Qing Gao
Journal: MedComm (2023)

Mesenchymal stem cell (MSC)-based therapies are flourishing. MSCs could be used as potential therapeutic agents for regenerative medicine due to their own repair function. Meanwhile, the natural predisposition toward inflammation or injury sites makes them promising carriers for targeted drug delivery. Inorganic nanoparticles (INPs) are greatly favored for their unique properties and potential applications in biomedical fields. Current research has integrated INPs with MSCs to enhance their regenerative or antitumor functions. This model also allows the in vivo fate tracking of MSCs in multiple imaging modalities, as many INPs are also excellent contrast agents. Thus, INP-integrated MSCs would be a multifunctional biologic agent with great potential. In this review, the current roles performed by the integration of INPs with MSCs, including (i) enhancing their repair and regeneration capacity via the improvement of migration, survival, paracrine, or differentiation properties, (ii) empowering tumor-killing ability through agent loaded or hyperthermia, and (iii) conferring traceability are summarized. An introduction of INP-integrated MSCs for simultaneous treatment and tracking is also included. The promising applications of INP-integrated MSCs in future treatments are emphasized and the challenges to their clinical translation are discussed.
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis
Authors: Markos Tesfaye, Piotr Jaholkowski, Guy F. L. Hindley, Alexey A. Shadrin, Zillur Rahman, Shahram Bahrami, Aihua Lin, Børge Holen, Nadine Parker, Weiqiu Cheng, Linn Rødevand, Oleksandr Frei, Srdjan Djurovic, Anders M. Dale, Olav B. Smeland, Kevin S. O’Connell, Ole A. Andreassen
Journal: Genome Medicine (2023)

Abstract Background Irritable bowel syndrome (IBS) often co-occurs with psychiatric and gastrointestinal disorders. A recent genome-wide association study (GWAS) identified several genetic risk variants for IBS. However, most of the heritability remains unidentified, and the genetic overlap with psychiatric and somatic disorders is not quantified beyond genome-wide genetic correlations. Here, we characterize the genetic architecture of IBS, further, investigate its genetic overlap with psychiatric and gastrointestinal phenotypes, and identify novel genomic risk loci. Methods Using GWAS summary statistics of IBS (53,400 cases and 433,201 controls), and psychiatric and gastrointestinal phenotypes, we performed bivariate casual mixture model analysis to characterize the genetic architecture and genetic overlap between these phenotypes. We leveraged identified genetic overlap to boost the discovery of genomic loci associated with IBS, and to identify specific shared loci associated with both IBS and psychiatric and gastrointestinal phenotypes, using the conditional/conjunctional false discovery rate (condFDR/conjFDR) framework. We used functional mapping and gene annotation (FUMA) for functional analyses. Results IBS was highly polygenic with 12k trait-influencing variants. We found extensive polygenic overlap between IBS and psychiatric disorders and to a lesser extent with gastrointestinal diseases. We identified 132 independent IBS-associated loci (condFDR &lt; 0.05) by conditioning on psychiatric disorders ( n = 127) and gastrointestinal diseases ( n = 24). Using conjFDR, 70 unique loci were shared between IBS and psychiatric disorders. Functional analyses of shared loci revealed enrichment for biological pathways of the nervous and immune systems. Genetic correlations and shared loci between psychiatric disorders and IBS subtypes were different. Conclusions We found extensive polygenic overlap of IBS and psychiatric and gastrointestinal phenotypes beyond what was revealed with genetic correlations. Leveraging the overlap, we discovered genetic loci associated with IBS which implicate a wide range of biological pathways beyond the gut-brain axis. Genetic differences may underlie the clinical subtype of IBS. These results increase our understanding of the pathophysiology of IBS which may form the basis for the development of individualized interventions.
Harald zur Hausen, MD, FAACR: In Memoriam (1936–2023)
Authors: Frank Rösl
Journal: Cancer Research (2023)

Obituary| August 01 2023 Harald zur Hausen, MD, FAACR: In Memoriam (1936–2023) Frank Rösl 0009-0005-8572-8002 Frank Rösl * *Corresponding Author: Frank Rösl, Retired Head of Division Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Phone: 49-6221-42-4900; E-mail: f.roesl@dkfz.de; Foucault0306@web.de Search for other works by this author on: This Site PubMed Google Scholar Author & Article Information *Corresponding Author: Frank Rösl, Retired Head of Division Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Phone: 49-6221-42-4900; E-mail: ; Foucault0306@web.de Cancer Res 2023;83:2439–40 Online ISSN: 1538-7445 Print ISSN: 0008-5472 ©2023 American Association for Cancer Research2023American Association for Cancer Research Cancer Res (2023) 83 (15): 2439–2440. https://doi.org/10.1158/0008-5472.CAN-23-1979 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record August 1 2023 Citation Frank Rösl; Harald zur Hausen, MD, FAACR: In Memoriam (1936–2023). Cancer Res 1 August 2023; 83 (15): 2439–2440. https://doi.org/10.1158/0008-5472.CAN-23-1979 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search “What's new?” Everybody in the group of Harald zur Hausen was familiar with this question, even expecting it, and was ready to inform him about recent results during his short visits. Although he was constantly absorbed in many obligations and responsibilities after becoming the Scientific Director of the German Cancer Research Center (“Deutsches Krebsforschungszentrum, DKFZ”) in Heidelberg in May 1983, zur Hausen made his rounds through the laboratories every morning to interview his coworkers about their progress or eventual experimental difficulties. This kind of “science-in-progress information tour” was nourished by his incredible curiosity to understand the processes underlying the development of human cancer. On the basis of this daily laboratory walk, “zH”—everyone used these two magic letters at that time (and still today) when talking about him—was informed about every single experimental step of each PhD student or postdoctoral fellow in his group. Due to his phenomenal memory, he could... You do not currently have access to this content.
Transient ischaemic dilation ratio thresholds in patients with zero coronary calcium score undergoing exercise or dipyridamole stress SPECT myocardial perfusion imaging using a cadmium-zinc-telluride camera
Authors: Eran Wen Jun Sim, Min Sen Yew
Journal:  (2023)

Abstract Aims Transient ischaemic dilation (TID) is a marker of underlying extensive coronary artery disease (CAD) during myocardial perfusion imaging (MPI). The cut-off for a normal TID ratio (TIDr) value is often derived from a cohort of individuals with no apparent CAD. Varying criteria have been used to define the absence of CAD. We aim to derive TIDr cut-offs using patients with normal MPI and coronary artery calcium (CAC) score of zero, and compare the TIDr obtained from different software packages. Methods and results We studied 232 patients with zero CAC and normal MPI undergoing exercise or dipyridamole stress using either a 1- or 2-day protocol. All patients were scanned in the supine position with a cadmium-zinc-telluride camera. TIDr was automatically generated using quantitative perfusion SPECT (QPS) software initially, and subsequently using Myometrix for comparison. The TIDr cut-offs calculated using the mean + 2 standard deviation were 1.29 and 1.24 for the 1- and 2-day protocol groups, respectively. In patients undergoing a 2-day protocol, dipyridamole stress resulted in significantly higher mean TIDr when compared to exercise stress (1.07 ± 0.13 vs. 1.01 ± 0.12, P = 0.035). Myometrix-derived TIDr were also significantly lower compared to QPS-derived values for most protocols except for 2-day exercise stress. Conclusion This study is the first to derive TIDr threshold values using a normal population defined by zero CAC and normal MPI. TIDr was found to vary depending on stress modality, protocol as well as the software used.
Recurrent Haemothorax Secondary to the Aberrant Vessel and Rib Bone Spurs: Coincidence or Correlation? A Case Report
Authors: Adli Azam, Adli Azam, Aida AA
Journal: International Journal of Surgery (2023)

There are reports of spontaneous or recurrent haemothorax, in which an aberrant vessel or rib spur is the cause. We report a case of 13 years old male who presented twice with spontaneous haemothorax which bleeding from an aberrant vessel was the apparent cause on the first encounter and was later found to have a rib spur. He underwent left VATS procedure which was well tolerated without any complications.
Heavy-chain CDR3-engineered B cells facilitate in vivo evaluation of HIV-1 vaccine candidates
Authors: Wenhui He, Tianling Ou, Nickolas Skamangas, Charles C. Bailey, Naomi Bronkema, Yan Guo, Yiming Yin, Valerie Kobzarenko, Xia Zhang, Andi Pan, Xin Liu, Jinge Xu, Lizhou Zhang, Ava E. Allwardt, Debasis Mitra, Brian Quinlan, Rogier W. Sanders, Hyeryun Choe, Michael Farzan
Journal: Immunity (2023)
Liposomal <scp>AntagomiR</scp>‐155‐5p Restores <scp>Anti‐Inflammatory</scp> Macrophages and Improves Arthritis in Preclinical Models of Rheumatoid Arthritis
Authors: Audrey Paoletti, Bineta Ly, Catherine Cailleau, Fan Gao, Marie Péan de Ponfilly‐Sotier, Juliette Pascaud, Elodie Rivière, Luxin Yang, Lilian Nwosu, Aziza Elmesmari, Franceline Reynaud, Magali Hita, David Paterson, Julien Reboud, Francois Fay, Gaetane Nocturne, Nicolas Tsapis, Iain B. McInnes, Mariola Kurowska‐Stolarska, Elias Fattal, Xavier Mariette
Journal: Arthritis & Rheumatology (2023)

Objective We previously reported an increased expression of microRNA‐155 (miR‐155) in the blood monocytes of patients with rheumatoid arthritis (RA) that could be responsible for impaired monocyte polarization to anti‐inflammatory M2‐like macrophages. In this study, we employed two preclinical models of RA, collagen‐induced arthritis and K/BxN serum transfer arthritis, to examine the therapeutic potential of antagomiR‐155‐5p entrapped within PEGylated (polyethylene glycol [PEG]) liposomes in resolution of arthritis and repolarization of monocytes towards the anti‐inflammatory M2 phenotype. Methods AntagomiR‐155‐5p or antagomiR‐control were encapsulated in PEG liposomes of 100 nm in size and −10 mV in zeta potential with high antagomiR loading efficiency (above 80%). Mice were injected intravenously with 1.5 nmol/100 μL PEG liposomes containing antagomiR‐155‐5p or control after the induction of arthritis. Results We demonstrated the biodistribution of fluorescently tagged PEG liposomes to inflamed joints one hour after the injection of fluorescently tagged PEG liposomes, as well as the liver's subsequent accumulation after 48 hours, indicative of hepatic clearance, in mice with arthritis. The injection of PEG liposomes containing antagomiR‐155‐5p decreased arthritis score and paw swelling compared with PEG liposomes containing antagomiR‐control or the systemic delivery of free antagomiR‐155‐5p. Moreover, treatment with PEG liposomes containing antagomiR‐155‐5p led to the restoration of bone marrow monocyte defects in anti‐inflammatory macrophage differentiation without any significant functional change in other immune cells, including splenic B and T cells. Conclusion The injection of antagomiR‐155‐5p encapsulated in PEG liposomes allows the delivery of small RNA to monocytes and macrophages and reduces joint inflammation in murine models of RA, providing a promising strategy in human disease. image
Genome annotation: From human genetics to biodiversity genomics
Authors: Roderic Guigó
Journal: Cell Genomics (2023)

Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.
Corrigendum to “Nasopharyngeal swabs as alternative specimens for the diagnosis of dengue virus infection” [J Infect 87 (2023) 145–147]
Authors: Alícia Cavalcante Maia, Tatyane de Souza Cardoso Quintão, Pâmela Maria de Oliveira, Évelin Mota Cassemiro, Daiani Cristina Cilião-Alves, Priscilla Pedrette de Melo Alves, Fabiano dos Anjos Pereira Martins, Emerson Luiz Lima Araújo, Helen da Costa Gurgel, Elza Ferreira Noronha, Walter Massa Ramalho, Alex Leite Pereira, Svetoslav Nanev Slavov, Wildo Navegantes de Araújo, Rodrigo Haddad
Journal: Journal of Infection (2023)
The role of Janus kinase signaling in the pathology of atopic dermatitis
Authors: Emma Guttman-Yassky, Alan D. Irvine, Patrick M. Brunner, Brian S. Kim, Mark Boguniewicz, Julie Parmentier, Andrew M. Platt, Kenji Kabashima
Journal: Journal of Allergy and Clinical Immunology (2023)

Atopic dermatitis (AD) is a heterogeneous, chronic, relapsing, inflammatory skin disease associated with considerable physical, psychological, and economic burden. The pathology of AD includes complex interactions involving abnormalities in immune and skin barrier genes, skin barrier disruption, immune dysregulation, microbiome disturbance, and other environmental factors. Many of the cytokines involved in AD pathology, including IL-4, IL-13, IL-22, IL-31, thymic stromal lymphopoietin, and IFN-γ, signal through the Janus kinase (JAK)-signal transducer and activation of transcription (STAT) pathway. The JAK family includes JAK1, JAK2, JAK3, and tyrosine kinase 2; the STAT family includes STAT1, STAT2, STAT3, STAT4, STAT5A/B, and STAT6. Activation of the JAK-STAT pathway has been implicated in the pathology of several immune-mediated inflammatory diseases, including AD. However, the exact mechanisms of JAK-STAT involvement in AD have not been fully characterized. This review aims to discuss current knowledge about the role of the JAK-STAT signaling pathway and, specifically, the role of JAK1 in the pathology and symptomology of AD.
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
Authors: Francisco Avila Cobos, Mohammad Javad Najaf Panah, Jessica Epps, Xiaochen Long, Tsz-Kwong Man, Hua-Sheng Chiu, Elad Chomsky, Evgeny Kiner, Michael J. Krueger, Diego di Bernardo, Luis Voloch, Jan Molenaar, Sander R. van Hooff, Frank Westermann, Selina Jansky, Michele L. Redell, Pieter Mestdagh, Pavel Sumazin
Journal: Genome biology (2023)

Abstract Background RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues and reveal cells that influence key functions in both healthy and disease tissues. However, the use of these technologies is operationally challenging because of high costs and stringent sample-collection requirements. Computational deconvolution methods that infer the composition of bulk-profiled samples using scnRNA-seq-characterized cell types can broaden scnRNA-seq applications, but their effectiveness remains controversial. Results We produced the first systematic evaluation of deconvolution methods on datasets with either known or scnRNA-seq-estimated compositions. Our analyses revealed biases that are common to scnRNA-seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-seq and scnRNA-seq profiles can help improve the accuracy of both scnRNA-seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), which combines RNA-seq transformation and dampened weighted least-squares deconvolution approaches, consistently outperformed other methods in predicting the composition of cell mixtures and tissue samples. Conclusions We showed that analysis of concurrent RNA-seq and scnRNA-seq profiles with SQUID can produce accurate cell-type abundance estimates and that this accuracy improvement was necessary for identifying outcomes-predictive cancer cell subclones in pediatric acute myeloid leukemia and neuroblastoma datasets. These results suggest that deconvolution accuracy improvements are vital to enabling its applications in the life sciences.
Reducing the Risks of Nuclear War
Authors: Dost Öngür
Journal: JAMA Psychiatry (2023)

Kamran Abbasi; Parveen Ali; Virginia Barbour; Kirsten Bibbins-Domingo; Marcel G.M. Olde Rikkert; Andy Haines; Ira Helfand; Richard Horton; Bob Mash; Arun Mitra; Carlos Monteiro; Elena N. Naumova; Eric J. Rubin; Tilman Ruff; Peush Sahni; James Tumwine; Paul Yonga; Chris Zielinski
Reducing the risks of nuclear war
Authors: Kamran Abbasi, Parveen Ali, Virginia Barbour, Kirsten Bibbins-Domingo, Marcel G M Olde Rikkert, Andy Haines, Ira Helfand, Richard Horton, Bob Mash, Arun Mitra, Carlos Monteiro, Elena N Naumova, Eric J Rubin, Tilman Ruff, Peush Sahni, James Tumwine, Paul Yonga, Chris Zielinski
Journal: BMJ (2023)
Designing clinical trials based on modern imaging and metastasis-directed treatments in patients with oligometastatic breast cancer: a consensus recommendation from the EORTC Imaging and Breast Cancer Groups
Authors: David Pasquier, Luc Bidaut, Daniela Elena Oprea-Lager, Nandita M deSouza, David Krug, Laurence Collette, Wolfgang Kunz, Yazid Belkacemi, Maria Grazia Bau, Caroline Caramella, Lioe-Fee De Geus-Oei, Alex De Caluwé, Christophe Deroose, Olivier Gheysens, Ken Herrmann, Isabelle Kindts, Michalis Kontos, Sherko Kümmel, Barbro Linderholm, Egesta Lopci, Icro Meattini, Ann Smeets, Orit Kaidar-Person, Philip Poortmans, Pelagia Tsoutsou, Nawale Hajjaji, Nicola Russell, Elżbieta Senkus, Jean-Noël Talbot, Lale Umutlu, Vincent Vandecaveye, Joost J C Verhoeff, Willemien Menke-van der Houven van Oordt, Helle D Zacho, Fatima Cardoso, Laure Fournier, Frederieke Van Duijnhoven, Frédéric E Lecouvet
Journal: The Lancet Oncology (2023)
Artificial intelligence-supported screen reading versus standard double reading in the Mammography Screening with Artificial Intelligence trial (MASAI): a clinical safety analysis of a randomised, controlled, non-inferiority, single-blinded, screening accuracy study
Authors: Kristina Lång, Viktoria Josefsson, Anna-Maria Larsson, Stefan Larsson, Charlotte Högberg, Hanna Sartor, Solveig Hofvind, Ingvar Andersson, Aldana Rosso
Journal: The Lancet Oncology (2023)
Changes in cancer diagnoses and stage distribution during the first year of the COVID-19 pandemic in the USA: a cross-sectional nationwide assessment
Authors: Xuesong Han, Nuo Nova Yang, Leticia Nogueira, Changchuan Jiang, Nikita Sandeep Wagle, Jingxuan Zhao, Kewei Sylvia Shi, Qinjin Fan, Elizabeth Schafer, K Robin Yabroff, Ahmedin Jemal
Journal: The Lancet Oncology (2023)
Nasogastric-tube decompression facilitates the pocket-creation method of gastric endoscopic submucosal dissection.
Authors: Hisashi Fukuda, Yoshikazu Hayashi, Yuka Kowazaki, Takaaki Morikawa, Alan Kawarai Lefor, Tetsurou Miwata, Sawako Fujikura
Journal: Endoscopy (2023)

The pocket-creation method (PCM) [1] was developed as an effective strategy for endoscopic submucosal dissection (ESD), and its usefulness in gastric ESD has been reported [2].
Radiotherapy resources in Brazil (RT2030): a comprehensive analysis and projections for 2030
Authors: Arthur Accioly Rosa, Cecília Félix Penido Mendes de Sousa, Leonardo Cunha Furbino Pimentel, Homero Lavieri Martins, Fabio Ynoe Moraes, Gustavo Nader Marta, Marcus Simões Castilho
Journal: The Lancet Oncology (2023)
National Cancer Institute Collaborative Workshop on Shaping the Landscape of Brain Metastases Research: challenges and recommended priorities
Authors: Michelle M Kim, Minesh P Mehta, DeeDee K Smart, Patricia S Steeg, Julie A Hong, Michael G Espey, Pataje G Prasanna, Laura Crandon, Christine Hodgdon, Niki Kozak, Terri S Armstrong, Aki Morikawa, Nicole Willmarth, Kirk Tanner, Adrienne Boire, Melanie Hayden Gephart, Kim A Margolin, Jona Hattangadi-Gluth, Hussein Tawbi, Daniel M Trifiletti, Caroline Chung, Upal Basu-Roy, Robyn Burns, Isabella C Glitza Oliva, Ayal A Aizer, Carey K Anders, Joanne Davis, Manmeet S Ahluwalia, Veronica Chiang, Jing Li, Rupesh Kotecha, Silvia C Formenti, Benjamin M Ellingson, Vinai Gondi, Paul W Sperduto, Jill S Barnholtz-Sloan, Jordi Rodon, Eudocia Q Lee, Mustafa Khasraw, Debra Nana Yeboa, Priscilla K Brastianos, Evanthia Galanis, C Norman Coleman, Mansoor M Ahmed
Journal: The Lancet Oncology (2023)
One-step endoscopic ultrasound-guided fine-needle biopsy of pancreatic mass, gastroenterostomy, and gallbladder drainage for malignant biliary and gastric outlet obstruction
Authors: Benedetto Mangiavillano, Luca Brandaleone, Francesco Auriemma, Federica Calabrese, Danilo Paduano, Carmine S. Gentile, Alessandro Repici
Journal: Endoscopy (2023)

A 77-year-old woman was admitted to our emergency department because of a 2-week history of vomiting, weight loss, and abdominal pain. An abdominal computed tomography (CT) scan revealed a 4-cm pancreatic mass that resulted in gastric outlet obstruction and dilation of the biliary tree and gallbladder. In a multidisciplinary meeting, it was decided to perform endoscopic ultrasound (EUS)-guided fine-needle biopsy (EUS-FNB), EUS-guided gastroenterostomy (EUS-GE), and EUS-guided gallbladder drainage (EUS-GBD) using two lumen-apposing metal stents (LAMSs). Under general anesthesia, EUS-FNB of the pancreatic mass was performed through the stomach using a 22-G needle (Acquire; Boston Scientific, Natick, Massachusetts, USA) ([Video 1]). Subsequently, a nasobiliary tube was passed through the neoplastic stricture to fill the jejunal loop with saline solution, methylene blue, and contrast medium. A 16 × 20-mm electrocautery-enhanced LAMS (Hot-Spaxus; Taewoong Medical, Gimpo-si, Korea) was passed from the stomach to the dilated jejunal loop using the freehand technique ([Fig. 1]). The proximal flange of the LAMS was deployed using the intrachannel technique. Subsequently, EUS-GBD was performed using an 8 × 20-mm electrocautery-enhanced LAMS (Hot-Spaxus; Taewoong Medical) and the freehand technique ([Fig. 2]). No adverse events were experienced by the patient. The post-procedural CT scan confirmed the accurate positioning of the two LAMSs between the stomach and jejunum, and between the stomach and gallbladder. The patient was discharged after 3 days, having successfully resumed oral feeding. In conclusion, in such cases, a one-step approach involving EUS-FNB, EUS-GE, and EUS-GBD is safe when performed by experts ([Video 1]).